It certainly doesn't have to be in the Steam install folder. It appears you installed it into the SH3 game foldere there. I don't think it can harm anything. But having it installed into the Program Files folder requires you to run it as administrator. Not doing this in Windows 7 or Vista might cause problems. (though I don't know how that second running instance of SH3 Commander plays into this) I suggest you install SH3 Commander somewhere else entirely (like c:\Games\SH3 Commander) and see how it fares then.
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